Limited Dissolve and face loop selection
Okay, so @Denis definitely put me down the correct path. So, when using Limited Dissolve, it does create N-Polygons.

So, eventually I managed to stumble across https://blenderartists.org/forum/showthread.php?254109-convert-n-gon-to-quads-tris . I'd highly recommend adding the plugin to blender, which when activated, under the 'Object Data' tab, it will count the number of Ngons, Quads, and Tris for you.

Anyways, so when I clicked 'Select ngons' they popped right up nice and highlighted. I then converted the ngons to triangles, then back to quads, and that seemed to clean things up.

Just wanted to update this post, should anyone come across this.